WO2019165237A1 - Sequencing method for car t cell therapy - Google Patents

Sequencing method for car t cell therapy Download PDF

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Publication number
WO2019165237A1
WO2019165237A1 PCT/US2019/019191 US2019019191W WO2019165237A1 WO 2019165237 A1 WO2019165237 A1 WO 2019165237A1 US 2019019191 W US2019019191 W US 2019019191W WO 2019165237 A1 WO2019165237 A1 WO 2019165237A1
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WIPO (PCT)
Prior art keywords
compound
pharmaceutically acceptable
acceptable salt
car
dose
Prior art date
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Ceased
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PCT/US2019/019191
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English (en)
French (fr)
Inventor
Richard Messmann
Christopher Paul Leamon
Haiyan CHU
Yingjuan June Lu
Philip Stewart Low
Michael C. Jensen
James MATTHAEI
Navin Robert Charles PINTO
Julie Ruggieri PARK
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Seattle Childrens Hospital
Purdue Research Foundation
Endocyte Inc
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Seattle Childrens Hospital
Purdue Research Foundation
Endocyte Inc
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Priority to JP2020544671A priority Critical patent/JP7568224B2/ja
Priority to EP19757681.2A priority patent/EP3755366A4/en
Priority to CA3091674A priority patent/CA3091674A1/en
Priority to AU2019225174A priority patent/AU2019225174B2/en
Priority to US16/971,801 priority patent/US12240870B2/en
Priority to CN201980027953.8A priority patent/CN112105382A/zh
Application filed by Seattle Childrens Hospital, Purdue Research Foundation, Endocyte Inc filed Critical Seattle Childrens Hospital
Publication of WO2019165237A1 publication Critical patent/WO2019165237A1/en
Anticipated expiration legal-status Critical
Priority to JP2024091419A priority patent/JP2024178129A/ja
Priority to US18/963,158 priority patent/US20250230216A1/en
Priority to AU2026201166A priority patent/AU2026201166A1/en
Ceased legal-status Critical Current

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    • C07—ORGANIC CHEMISTRY
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    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/44—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material not provided for elsewhere, e.g. haptens, metals, DNA, RNA, amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/31—Chimeric antigen receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
    • A61K40/4203—Receptors for growth factors
    • A61K40/4204—Epidermal growth factor receptors [EGFR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/429—Small organic molecules e.g. cocaine or nicotine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/55—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug
    • A61K47/551—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug one of the codrug's components being a vitamin, e.g. niacinamide, vitamin B3, cobalamin, vitamin B12, folate, vitamin A or retinoic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
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    • C07—ORGANIC CHEMISTRY
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/38—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the dose, timing or administration schedule
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    • C07—ORGANIC CHEMISTRY
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    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/40—Immunoglobulins specific features characterized by post-translational modification
    • C07K2317/41—Glycosylation, sialylation, or fucosylation
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    • C07K2317/00—Immunoglobulins specific features
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    • C07K2317/52—Constant or Fc region; Isotype
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    • C07—ORGANIC CHEMISTRY
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    • C07K2317/00—Immunoglobulins specific features
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    • C07K2317/524—CH2 domain
    • C—CHEMISTRY; METALLURGY
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/72—Increased effector function due to an Fc-modification
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/33—Fusion polypeptide fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies
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    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • the present disclosure relates to methods of treating a patient with a cancer by administering to the patient a composition comprising CAR T cells and administering to the patient a small molecule linked to a targeting moiety by a linker.
  • the disclosure also relates to compositions for use in such methods.
  • X 1 and Y 1 are each-independently selected from the group consisting of halo, R 2 , OR 2 , SR 3 , and NR 4 R 5 ;
  • Q is selected from the group consisting of C and CH;
  • FIG. 12 shows EC17 dose finding and CRS assessment in tumor versus tumor- free mice.
  • Panel A Schematic diagram to show dose scheduling of CAR-T cells (-10 million “clinical facsimile”) plus EC17 dosed 3 different ways in NSG mice without or with pre- established MDA-MB-231 xenografts. Tumor- free mice received EC 17 SIW 500 nmol/kg (2 doses on days 2 and 10).
  • FIG. 13 shows EC17 dose escalation in safety and anti-leukemic activity in-vivo.
  • Panel A Schematic diagrams to show dose scheduling of EC 17 plus unsorted EGFRt CAR-T cells ( ⁇ 6 million, day 0) in NSG mice with l-day-old intravenous THP 1 -FRf) xenografts.
  • the ligand is a ligand of gamma glutamyl transpeptidase.
  • the targeting moiety is selected from the group consisting of 2,4-dinitrophenol (DNP), 2,4,6-trinitrophenol (TNP), biotin, digoxigenin, fluorescein, fluorescein isothiocyanate (FITC), NHS-fluorescein, pentafluorophenyl ester, tetrafluorophenyl ester, a knottin, a centyrin, and a DARPin.
  • n is an integer from 0 to 200.
  • p, r, s, and t are each independently either 0 or 1;
  • the“targeting moiety” that binds to the CAR expressed by CAR T cells can be selected, for example, from 2,4-dinitrophenol (DNP), 2,4,6-trinitrophenol (TNP), biotin, digoxigenin, fluorescein, fluorescein isothiocyanate (FITC), NHS-fluorescein, pentafluorophenyl ester, tetrafluorophenyl ester, a knottin, a centyrin, a DARPin, an affibody, an affilin, an anticalin, an atrimer, an avimer, a bicicyclic peptide, an FN3 scaffold, a cys-knot, a fynomer, a Kunitz domain, or an Obody.
  • DNP 2,4-dinitrophenol
  • TNP 2,4,6-trinitrophenol
  • biotin digoxigenin
  • fluorescein fluorescein isothiocyanate
  • targeting moiety is limited only in that it should be recognized and bound by the CAR, preferably with specificity, and that it has a relatively low molecular weight.
  • exemplary targeting moieties are haptens, including small molecular weight organic molecules.
  • the T lymphocytes can be obtained from a patient by means well- known in the art.
  • T cells e.g., cytotoxic T cells
  • T cells can be obtained by collecting peripheral blood from the patient, subjecting the blood to Ficoll density gradient centrifugation, and then using a negative T cell isolation kit (such as EasySepTM T Cell Isolation Kit) to isolate a population of T cells from the peripheral blood.
  • the population of T lymphocytes e.g., cytotoxic T cells
  • the population being collected can comprise at least about 90% of the selected cell type, at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the selected cell type.
  • R 6 and R 7 are each independently selected from the group consisting of hydrogen, halo, Ci-Ci 2 alkyl, and Ci-Ci 2 alkoxy; or, R 6 and R 7 are taken together to form a carbonyl group;
  • the CAR T cells can persist in elevated numbers of circulating CAR T cells for as long as about 10 days, as long as about 15 days, as long as about 20 days, as long as about 25 days, as long as about 30 days, as long as about 35 days, as long as about 40 days, as long as about 45 days, as long as about 50 days, as long as about 55 days, as long as about 60 days, as long as about 65 days, as long as about 70 days, as long as about 75 days, or as long as about 80 days post CAR T cell administration ⁇
  • Fmoc deprotection was carried out using 20% piperidine in DMF (3 x 10 mL), before each amino acid coupling. The above sequence was repeated to complete reaction with 2X Fmoc-PEG36-COOH (161 mg, 1.0 equiv), Fmoc-Glu- OtBu (72 mg, 2.0 equiv ) and Tfa.Pteroic-acid ( 41.0 mg, 1.2 equiv) coupling steps.
  • the pure fractions were collected, all organic solvents were evaporated and the sample was lyophilized for 48 h to provide the NKl-PEGn-NHBoc. Yield: 40.13 mg (97%).
  • DUPA-FITC was synthesized by solid phase methodology as follows. Universal NovaTag resin (50 mg, 0.53 mM) was swollen with dichloromethane (DCM) (3 mL) followed by dimethylformamide (DMF, 3 mL). A solution of 20% piperidine in DMF (3 x 3 mL) was added to the resin, and argon was bubbled for 5 min. The resin was washed with DMF (3 x 3 mL) and isopropyl alcohol (i-PrOH, 3 x 3 mL).
  • DCM dichloromethane
  • DMF dimethylformamide
  • T cells Under chronic antigen stimulation, for example in instances of chronic viral infections or cancer, T cells undergo a process of exhaustion where they are no longer able to proliferate, secrete inflammatory cytokines or kill antigen presenting target cells. CAR T cells also possess the potential for exhaustion under chronic stimulation of the CAR by constant presence of scFv stimulating antigen. Because our E2 CAR T cells only react to the presence of our bridge molecule, EC17, bound to the surface of FR+ tumor cells, we have the ability to prevent chronic antigen stimulation of the E2 CAR T cells by ceasing treatment with EC 17 and hence removing the presence of surface bound antigen. The rest period characterized by the absense of surface antigen prevents chronic antigen exposure of E2 CAR T cells and prevents the resulting exhaustion that could result.
  • a fluorophore-conjugated anti-biotin was also purchased from BioLegend.
  • APC-conjugated anti- FITC mouse IgG2a/kappa antibody (clone NAWESLEE), CountBrightTM beads (Invitrogen), Annexin V staining buffer, and AlexaFluor-647-conjugated Annexin V were purchased from Thermo Fisher Scientific.
  • collagenase IV, hyaluronidase and DNase I were all purchased from Sigma-Aldrich (St. Louis, MO).
  • EC17 or folate-FITC [FA-(y)-ethylenediamine-FITC] was synthesized at Endocyte.
  • CD4/CD8 This batch of CAR-T cells consisted of mostly TSCM and TCM phenotypes (see Figure 9).
  • Two days after the CAR-T cell injection one cohort of tumor-bearing mice were left untreated while three cohorts were treated with different regimens of EC 17, including single injection per week (SIW) at 500 nmol/kg, or as escalating EC 17 dose levels of 5/50/500 (Escalation- 1) or 5/100/1000 nmol/kg (Escalation-2) given on a Monday/Thursday/Monday schedule with l-week drug-free intervals.
  • SIW single injection per week
  • two tumor-free cohorts were either untreated or treated with EC 17 SIW at 500 nmol/kg.

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PCT/US2019/019191 2018-02-23 2019-02-22 Sequencing method for car t cell therapy Ceased WO2019165237A1 (en)

Priority Applications (9)

Application Number Priority Date Filing Date Title
EP19757681.2A EP3755366A4 (en) 2018-02-23 2019-02-22 Sequencing method for car t cell therapy
CA3091674A CA3091674A1 (en) 2018-02-23 2019-02-22 Sequencing method for car t cell therapy
AU2019225174A AU2019225174B2 (en) 2018-02-23 2019-02-22 Sequencing method for CAR T cell therapy
US16/971,801 US12240870B2 (en) 2018-02-23 2019-02-22 Sequencing method for CAR T cell therapy
CN201980027953.8A CN112105382A (zh) 2018-02-23 2019-02-22 用于car t细胞疗法的顺序方法
JP2020544671A JP7568224B2 (ja) 2018-02-23 2019-02-22 Ｃａｒ ｔ細胞療法のための配列決定法
JP2024091419A JP2024178129A (ja) 2018-02-23 2024-06-05 Ｃａｒ ｔ細胞療法のための配列決定法
US18/963,158 US20250230216A1 (en) 2018-02-23 2024-11-27 Sequencing method for car t cell therapy
AU2026201166A AU2026201166A1 (en) 2018-02-23 2026-02-17 Sequencing method for CAR T cell therapy

Applications Claiming Priority (8)

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US201862634573P 2018-02-23 2018-02-23
US62/634,573 2018-02-23
US201862656265P 2018-04-11 2018-04-11
US62/656,265 2018-04-11
US201862724345P 2018-08-29 2018-08-29
US62/724,345 2018-08-29
US201862736730P 2018-09-26 2018-09-26
US62/736,730 2018-09-26

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US16/971,801 A-371-Of-International US12240870B2 (en) 2018-02-23 2019-02-22 Sequencing method for CAR T cell therapy
US18/963,158 Continuation US20250230216A1 (en) 2018-02-23 2024-11-27 Sequencing method for car t cell therapy

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AU (2) AU2019225174B2 (https=)
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Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3743082A4 (en) * 2018-01-22 2021-11-03 Seattle Children's Hospital (DBA Seattle Children's Research Institute) METHOD OF USE FOR CAR-T CELLS
WO2022118277A1 (en) * 2020-12-03 2022-06-09 Vilnius University Carbonic anhydrase inhibitors synthesized on interconnecting linker chains
JP2023513157A (ja) * 2020-02-04 2023-03-30 シアトル チルドレンズ ホスピタル （ディービーエイ シアトル チルドレンズ リサーチ インスティテュート） 抗ジニトロフェノールキメラ抗原受容体
US11759480B2 (en) 2017-02-28 2023-09-19 Endocyte, Inc. Compositions and methods for CAR T cell therapy
WO2024086563A1 (en) * 2022-10-19 2024-04-25 Seattle Children's Hospital (dba Seattle Children's Research Institute) Therapeutic methods with target-linked small molecules and anti-target car t cells
US12144850B2 (en) 2016-04-08 2024-11-19 Purdue Research Foundation Methods and compositions for car T cell therapy
US12150981B2 (en) 2012-12-20 2024-11-26 Purdue Research Foundation Chimeric antigen receptor-expressing T cells as anti-cancer therapeutics
US12240870B2 (en) 2018-02-23 2025-03-04 Purdue Research Foundation Sequencing method for CAR T cell therapy

Citations (2)

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Publication number Priority date Publication date Assignee Title
WO2016149665A1 (en) * 2015-03-18 2016-09-22 Baylor College Of Medicine Her2/erbb2 chimeric antigen receptor
WO2017177149A2 (en) * 2016-04-08 2017-10-12 Purdue Research Foundation Methods and compositions for car t cell therapy

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